[med-svn] [Git][med-team/flye][master] 2 commits: finish patching out six
Alexandre Detiste (@detiste-guest)
gitlab at salsa.debian.org
Sun Nov 23 19:41:01 GMT 2025
Alexandre Detiste pushed to branch master at Debian Med / flye
Commits:
2af7a527 by Alexandre Detiste at 2025-11-23T20:39:14+01:00
finish patching out six
- - - - -
ffb0cb33 by Alexandre Detiste at 2025-11-23T20:40:39+01:00
release
- - - - -
4 changed files:
- debian/changelog
- debian/control
- + debian/patches/patch_out_six.patch
- debian/patches/series
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,13 @@
+flye (2.9.6+dfsg-2) unstable; urgency=medium
+
+ * Team Upload
+ * Rewrite d/rules with shorter syntax
+ * Drop "Rules-Requires-Root: no": it is now the default
+ * Trim-out python3.12 patch
+ * Finish patching out six
+
+ -- Alexandre Detiste <tchet at debian.org> Sun, 23 Nov 2025 20:39:21 +0100
+
flye (2.9.6+dfsg-1) unstable; urgency=medium
* New upstream version 2.9.6+dfsg
=====================================
debian/control
=====================================
@@ -22,7 +22,6 @@ Architecture: any
Depends: ${shlibs:Depends},
${python3:Depends},
${misc:Depends},
- python3-six,
minimap2,
samtools
Description: de novo assembler for single molecule sequencing reads using repeat graphs
=====================================
debian/patches/patch_out_six.patch
=====================================
@@ -0,0 +1,175 @@
+--- a/flye/assembly/scaffolder.py
++++ b/flye/assembly/scaffolder.py
+@@ -12,7 +12,6 @@
+
+ import flye.utils.fasta_parser as fp
+ import flye.config.py_cfg as cfg
+-from six import iteritems
+
+ logger = logging.getLogger()
+
+@@ -128,7 +127,7 @@
+ contigs_stats[tokens[0]].coverage = tokens[2]
+
+ scaffolds_stats = {}
+- for scf, scf_seq in iteritems(scaffolds):
++ for scf, scf_seq in scaffolds.items():
+ scaffolds_stats[scf] = SeqStats(scf)
+ scf_length = sum([int(contigs_stats[unsigned(c)].length) for c in scf_seq])
+ scf_length += (len(scf_seq) - 1) * cfg.vals["scaffold_gap"]
+--- a/flye/config/configurator.py
++++ b/flye/config/configurator.py
+@@ -12,7 +12,6 @@
+
+ import flye.utils.fasta_parser as fp
+ import flye.config.py_cfg as cfg
+-from six import iteritems
+
+
+ logger = logging.getLogger()
+@@ -37,7 +36,7 @@
+ passing_reads = 0
+
+ for read_file in args.reads:
+- for _, seq_len in iteritems(fp.read_sequence_lengths(read_file)):
++ for _, seq_len in fp.read_sequence_lengths(read_file).items():
+ if seq_len > MAX_READ_LEN:
+ raise ConfigException("Length of single read in '{}' exceeded maximum ({})".format(read_file, MAX_READ_LEN))
+ if seq_len > lowest_read_len:
+--- a/flye/polishing/alignment.py
++++ b/flye/polishing/alignment.py
+@@ -18,7 +18,6 @@
+ import flye.utils.fasta_parser as fp
+ from flye.utils.utils import which, get_median
+ from flye.utils.sam_parser import AlignmentException
+-from six import iteritems
+
+
+
+@@ -47,7 +46,7 @@
+ def get_contigs_info(contigs_file):
+ contigs_info = {}
+ contigs_fasta = fp.read_sequence_dict(contigs_file)
+- for ctg_id, ctg_seq in iteritems(contigs_fasta):
++ for ctg_id, ctg_seq in contigs_fasta.items():
+ contig_type = ctg_id.split("_")[0]
+ contigs_info[ctg_id] = ContigInfo(ctg_id, len(ctg_seq),
+ contig_type)
+--- a/flye/polishing/consensus.py
++++ b/flye/polishing/consensus.py
+@@ -11,7 +11,6 @@
+ import logging
+ from collections import defaultdict
+
+-from six import itervalues
+
+ import multiprocessing
+ import traceback
+@@ -160,10 +159,10 @@
+ pos_nucl = elem.nucl
+
+ ins_group.clear()
+- for ins_str in itervalues(pos_insertions):
++ for ins_str in pos_insertions.values():
+ ins_group[ins_str] += 1
+
+- match_and_del_num = sum(itervalues(pos_matches))
++ match_and_del_num = sum(pos_matches.values())
+ del_num = pos_matches["-"]
+ num_ins = len(pos_insertions)
+
+--- a/flye/polishing/polish.py
++++ b/flye/polishing/polish.py
+@@ -21,7 +21,6 @@
+ import flye.utils.fasta_parser as fp
+ from flye.utils.utils import which
+ import flye.config.py_cfg as cfg
+-from six import iteritems
+
+
+
+@@ -329,7 +328,7 @@
+ polished_fasta = {}
+ polished_stats = {}
+ polished_coverages = {}
+- for ctg_id, seqs in iteritems(consensuses):
++ for ctg_id, seqs in consensuses.items():
+ seqs.sort(key=lambda p: (p[0], p[1]))
+ sorted_seqs = [p[3] for p in seqs]
+ bubble_coverages = [(len(p[3]), p[2]) for p in seqs]
+--- a/flye/short_plasmids/circular_sequences.py
++++ b/flye/short_plasmids/circular_sequences.py
+@@ -9,7 +9,6 @@
+ import flye.utils.fasta_parser as fp
+ from flye.utils.sam_parser import read_paf, read_paf_grouped
+ import logging
+-from six import iteritems
+
+
+ logger = logging.getLogger()
+@@ -47,7 +46,7 @@
+ def trim_circular_reads(circular_reads, unmapped_reads):
+ trimmed_circular_reads = dict()
+
+- for i, (read, hit) in enumerate(iteritems(circular_reads)):
++ for i, (read, hit) in enumerate(circular_reads.items()):
+ sequence = unmapped_reads[read][:hit.target_start].upper()
+ trimmed_circular_reads["circular_read_" + str(i)] = sequence
+
+--- a/flye/short_plasmids/unmapped_reads.py
++++ b/flye/short_plasmids/unmapped_reads.py
+@@ -9,7 +9,6 @@
+ from flye.utils.sam_parser import read_paf_grouped
+ import logging
+ from collections import defaultdict
+-from six import iteritems
+
+
+ logger = logging.getLogger()
+@@ -76,7 +75,7 @@
+ contigs = mapping_rates.get(hdr)
+ if contigs is not None:
+ is_unmapped = True
+- for _, mapping_rate in iteritems(contigs):
++ for _, mapping_rate in contigs.items():
+ if mapping_rate >= mapping_rate_threshold:
+ is_unmapped = False
+
+--- a/flye/trestle/graph_resolver.py
++++ b/flye/trestle/graph_resolver.py
+@@ -13,7 +13,6 @@
+
+ import flye.utils.fasta_parser as fp
+ from flye.repeat_graph.graph_alignment import iter_alignments
+-from six import iteritems
+
+
+ logger = logging.getLogger()
+@@ -146,7 +145,7 @@
+
+ def dump_repeats(repeats_info, filename):
+ with open(filename, "w") as f:
+- for repeat_id, info in iteritems(repeats_info):
++ for repeat_id, info in repeats_info.items():
+ f.write("#Repeat {0}\t{1}\n\n".format(repeat_id, info.multiplicity))
+
+ f.write("#All reads\t{0}\n".format(len(info.all_reads)))
+--- a/flye/utils/sam_parser.py
++++ b/flye/utils/sam_parser.py
+@@ -33,7 +33,6 @@
+ _BYTES = str.encode
+
+
+-from six import iteritems
+
+ import flye.utils.fasta_parser as fp
+ from flye.utils.utils import get_median
+@@ -209,7 +208,7 @@
+
+ #self.shared_manager = multiprocessing.Manager()
+ self.ref_fasta = dict() if multiproc_manager == None else multiproc_manager.dict()
+- for (h, s) in iteritems(reference_fasta):
++ for (h, s) in reference_fasta.items():
+ self.ref_fasta[_BYTES(h)] = _BYTES(s)
+
+ def get_region_sequence(self, region_id, region_start=None, region_end=None):
=====================================
debian/patches/series
=====================================
@@ -2,3 +2,4 @@ use_debian_packaged_libs.patch
cppflags.patch
python3.12.patch
distutils.patch
+patch_out_six.patch
View it on GitLab: https://salsa.debian.org/med-team/flye/-/compare/54ee6e5e631a619f224d2c42e139627158909ce1...ffb0cb334cc412ec7a066ef72ce4f52a4b399848
--
View it on GitLab: https://salsa.debian.org/med-team/flye/-/compare/54ee6e5e631a619f224d2c42e139627158909ce1...ffb0cb334cc412ec7a066ef72ce4f52a4b399848
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